It would be better to start using it straight away on a project if you are going to use it. It may be easier to get the hang of with less files.
You can add any files you want to your version control but source code and documentation are what it normally saved, in my experience.
To deploy a version of your system you usually check it out and tag the branch as a release. Then upload the files as normal.
Version control systems can do lots of useful things, I am no expert. I would recommend get yourself a good book on the subject and experiment with a small project first.
Adam